GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Fimbrial - Fimbrial protein
Pfam: PF00419 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0204
Length: 145
Sequences: 3697
Seq/Len: 25.5
HH_delta: 0.2 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
84_I119_A0.708622.967
121_L134_F0.671742.813
85_R120_R0.632972.650
87_S120_R0.616882.583
85_R122_V0.587222.459
42_T116_P0.572142.396
71_Y83_G0.570982.391
21_I41_F0.538952.257
16_N46_D0.503042.106
81_G129_I0.501652.100
42_T114_Q0.499612.092
72_L138_A0.47822.002
61_S141_T0.469281.965
44_T114_Q0.469011.964
16_N44_T0.46261.937
23_F121_L0.460531.928
40_P118_K0.446011.868
95_T98_N0.425061.780
84_I136_A0.421341.764
88_D92_Q0.420841.762
38_P120_R0.413431.731
24_G39_K0.399041.671
56_I142_V0.390221.634
23_F134_F0.38051.593
71_Y122_V0.373991.566
74_N134_F0.372651.560
59_T143_T0.3611.512
24_G134_F0.359661.506
72_L96_L0.357881.498
86_L117_F0.354551.485
57_K143_T0.347631.456
38_P118_K0.345361.446
40_P116_P0.34041.425
23_F84_I0.339771.423
31_L123_K0.328641.376
14_T46_D0.321681.347
32_S123_K0.313481.313
23_F39_K0.30941.295
72_L136_A0.307421.287
27_S30_D0.306231.282
85_R93_T0.305851.281
59_T99_P0.301111.261
58_L115_I0.299691.255
33_G123_K0.297511.246
41_F117_F0.290441.216
41_F140_F0.289781.213
91_G118_K0.282791.184
43_I140_F0.280251.173
31_L124_L0.275671.154
62_G72_L0.263991.105
16_N19_N0.263321.103
105_V108_S0.258311.082
28_T131_A0.254311.065
60_F117_F0.253981.063
35_T87_S0.251931.055
86_L138_A0.25121.052
100_F103_T0.245561.028
41_F119_A0.244871.025
21_I119_A0.244191.022
35_T120_R0.24371.020
82_V121_L0.241581.012
35_T85_R0.238110.997
65_D73_A0.237170.993
60_F86_L0.23550.986
10_P28_T0.234420.982
107_S110_N0.234420.982
94_I100_F0.232820.975
123_K129_I0.231890.971
38_P87_S0.228950.959
102_L105_V0.228830.958
124_L127_S0.228760.958
26_V134_F0.22460.940
57_K101_N0.222790.933
50_S54_N0.216360.906
59_T141_T0.214580.898
35_T122_V0.212120.888
89_S116_P0.2120.888
61_S97_N0.210690.882
17_V20_S0.209670.878
104_P107_S0.209080.875
96_L138_A0.208380.873
31_L82_V0.206530.865
31_L129_I0.20460.857
65_D68_D0.202990.850
26_V36_S0.202980.850
84_I134_F0.199770.836
119_A138_A0.199430.835
74_N121_L0.197450.827
43_I117_F0.194790.816
87_S118_K0.193580.811
45_L117_F0.191090.800
13_C47_C0.190750.799
97_N100_F0.189580.794
61_S98_N0.187840.787
43_I115_I0.186680.782
23_F119_A0.185950.779
31_L34_G0.185860.778
84_I138_A0.185240.776
76_N133_K0.185020.775
95_T99_P0.184740.774
70_N95_T0.183590.769
89_S93_T0.183580.769
12_T49_G0.182590.765
62_G65_D0.182340.763
140_F144_Y0.180910.757
74_N77_G0.179810.753
28_T129_I0.179260.751
83_G124_L0.178720.748
88_D94_I0.178420.747
54_N60_F0.17690.741
41_F86_L0.176240.738
30_D37_P0.175390.734
113_N116_P0.174610.731
23_F37_P0.172670.723
41_F60_F0.171190.717
9_V48_S0.166750.698
21_I39_K0.166720.698
22_D25_T0.166280.696
61_S139_T0.166020.695
12_T60_F0.165580.693
24_G37_P0.165390.693
57_K100_F0.16530.692
70_N74_N0.165010.691
69_N95_T0.164940.691
55_K104_P0.164730.690
74_N82_V0.164450.689
37_P121_L0.164380.688
12_T48_S0.164280.688
23_F120_R0.163990.687
67_S70_N0.163870.686
55_K107_S0.16370.685
12_T144_Y0.163680.685
71_Y85_R0.163440.684
27_S36_S0.163240.684
31_L121_L0.163140.683
60_F138_A0.160330.671
45_L113_N0.160320.671
16_N81_G0.159630.668
49_G93_T0.159260.667
15_I43_I0.159070.666
19_N44_T0.159030.666
90_N93_T0.158650.664
58_L120_R0.158320.663
81_G123_K0.157840.661
103_T106_N0.157610.660
45_L144_Y0.157270.659
10_P62_G0.156990.657
72_L75_T0.156950.657
30_D36_S0.156690.656
82_V130_T0.155950.653
34_G123_K0.155490.651
32_S125_S0.155450.651
100_F117_F0.154990.649
57_K118_K0.154720.648
117_F140_F0.15430.646
62_G71_Y0.154090.645
89_S118_K0.153980.645
84_I117_F0.153850.644
119_A141_T0.153320.642
81_G127_S0.15290.640
77_G130_T0.152830.640
75_T135_S0.152470.638
10_P50_S0.151930.636
82_V134_F0.151720.635
65_D69_N0.150530.630
15_I84_I0.150210.629
16_N78_D0.150170.629
69_N102_L0.150.628
22_D64_T0.149570.626
60_F94_I0.149440.626
60_F142_V0.149420.626
75_T78_D0.149410.626
10_P140_F0.149070.624
41_F84_I0.147460.617
63_N137_T0.147340.617
90_N106_N0.146970.615
108_S142_V0.146930.615
88_D98_N0.146450.613
15_I18_P0.145950.611
123_K128_T0.145920.611
101_N104_P0.145760.610
81_G128_T0.145430.609
65_D124_L0.144870.607
28_T140_F0.144020.603
132_G137_T0.143150.599
108_S113_N0.142920.598
87_S93_T0.142820.598
31_L144_Y0.142360.596
56_I59_T0.141940.594
34_G125_S0.141840.594
99_P102_L0.141790.594
27_S34_G0.140390.588
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
1pdkB0.972499.80.2
2jtyA0.965599.70.211
2jmrA0.951799.70.212
2w07B0.944899.70.224
2xg5B0.951799.70.23
2uy6B0.951799.70.248
4dwhB0.917299.70.281
3bwuF0.917299.60.288
3jwnH0.875999.60.317
3bfqG0.882899.60.318

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